Re: relax-users Digest, Vol 116, Issue 38 -- September 30, 2016 - 19:46

Sorry, I just want to make sure I fully understand this so I can explain it
to my PI:
So if there is symmetry, I can upload the same pdb file with the dimer (set
A and B) but tell it to read only one set. Since S^2 isn't effected too
much versus a dimer versus a monomer, the only thing that is important is
the change in co-ordinates of one set of the dimer (i.e. the differnence in
co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
or set A in a different version of that dimer's co-ordinates). I say this
because I have already run my protein's data with the pdb structure of the
monomer, and I have 2 different pdb files the docking program gave back for
the dimer (2 different ways the dimer could form from one interface).

Sincerely,
Sam

On Fri, Sep 30, 2016 at 10:29 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:

> Hi Sam,
>
> Please see below:
>
> > I'm a bit confused to that. If the protein is a dimer, and the tumbling
> > decreases, will that not results in altered  relaxation data?
>
> Yes.
>
> > Won't the
> > relaxation data average be higher, since it is relaxing slower due to its
> > increased size (tumbler slower in solution=slower relaxation back to
> > equilibrium)?
>
> No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
> affected too much, but it may decrease (maybe).  You need to
> understand how the diffusion tensor affects the J(w) spectral density
> curves to understand how R1 and the NOE will be affected.
>
>
> > Also, doesn't S^2 take into account the overall shape of the
> > molecule (as well as tensor type) in it's calculations?
>
> No.  The S2 value is the internal motions of the residue.  It is 100%
> independent of the global tumbling.
>
>
> > So won't a dimer
> > versus a monomer change the results just due to that?
>
> Not at all.  The optimised diffusion tensor should change, and the S2
> value stay the same.
>
>
> > So should I input both, read_mol=0 and read_mol=1?
>
> No, only one.  You can, however, perform a second analysis later with
> read_mol=1 (for comparison).
>
>
> > So
> > structure.read_pdb(file='cluster1_12.pdb', dir=None,
> >  read_mol=None, set_mol_name='hRGS4',
> > read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None,
> verbosity=1,
> > merge=False)
> > So mol_num=0 will be for chain A and mol_num=1 for chain B?
>
> This will have the same IndexError as before - relax will not handle
> two identical molecules in a model-free analysis at the same time.
> Again, this theory simply does not exist.  So I haven't added it to
> relax.  You need to perform the analysis on a single monomer of the
> homodimer.  But please check for symmetry - if you don't have
> symmetry, nobody on the planet can currently analyse non-symmetric
> homodimer data.
>
> Regards,
>
> Edward